Dear pymol users,
I am visualizing autodock vina results using PyMOL:
I open out.pdbqt (containing 9 docked conformations of ligand)
I open pr.pdb (containing protein structure)
I want to have 1 pdb file containing one of conformations of ligand
(for example number 1 which is the best pose) + pr
Hi Leila,
I can't reproduce your error. Your code works for me.
Did you try the following
save obj3.pdb, obj1_0001, obj2
Cheers,
Osvaldo
On Tue, Jul 14, 2015 at 5:02 AM, leila karami
wrote:
> Dear pymol users,
>
> I am visualizing autodock vina results using PyMOL:
>
> I open out.pdbqt (c
Dear Osvaldo,
I used 2 following ways:
1)
load out.pdbqt,obj1
load pr.pdb, obj2
split_states obj1
create obj3, (obj1_0001, obj2)
save obj3.pdb, obj3
2)
load out.pdbqt,obj1
load pr.pdb, obj2
split_states obj1
save obj3.pdb, (obj1_0001, obj2)
Unfortunately, in both cases, when I open obj3.pdb fil
Thanks. Heres how I did it:
import __main__
__main__.pymol_argv = ['pymol', '-qc']
import pymol
import os
from pymol import *
pymol.finish_launching()
one= '/protein_files/1A6M.pdb'
two = '/protein_files/1GZX.pdb'
name1 = os.path.basename(one)
name2 = os.path.basename(two)
# To get filename wit
Both methods work for me. Are you sure you are opening the correct obj3.pdb
file? Maybe you are saving the obj3.pdb file to a different directory and
opening an old obj3 file.
Wich PyMOL version are you using and on which operating system?
On Tue, Jul 14, 2015 at 10:25 AM, leila karami
wrote:
I am sure that I am in working directory. To prevent this mistake, I
selected desktop as working directory. (I put out.pdbqt and pr.pdb files in
desktop and then load them).
I am using pymol-0_99rc6-bin-win32 on windows 7.
My input files are as follows:
https://www.dropbox.com/s/hx94orra4pumx82/
Hi Leila,
Both methods works for me. You are using a really old PyMOL version. I
don't know if that is the problem but I think you should upgrade PyMOL.
Osvaldo
PS: Please use the reply button, to keep the whole conversation on the same
thread.
On Tue, Jul 14, 2015 at 10:49 AM, leila karami
wr
